Citation and License

BMC Genomics 2013, 14:29
doi:10.1186/1471-2164-14-29

Published: 16 January 2013

Abstract

Background

Reaumuria trigyna is an endangered small shrub endemic to desert regions in Inner Mongolia. This dicotyledonous
recretohalophyte has unique morphological characteristics that allow it to tolerate
the stress imposed by semi-desert saline soil. However, it is impossible to explore
the mechanisms underlying this tolerance without detailed genomic information. Fortunately,
newly developed high-throughput sequencing technologies are powerful tools for de novo sequencing to gain such information for this species.

Results

Two sequencing libraries prepared from control (C21) and NaCl-treated samples (T43)
were sequenced using short reads sequencing technology (Illumina) to investigate changes
in the R. trigyna transcriptome in response to salt stress. Among 65340 unigenes, 35495 (52.27%) were
annotated with gene descriptions, conserved domains, gene ontology terms, and metabolic
pathways with a cut-off E-value of 10-5. These included 44 Gene Ontology (GO) terms, 119 Kyoto Encyclopedia of Genes and
Genomes (KEGG) pathways, and 25 Clusters of Orthologous Groups families. By comparing
the transcriptomes from control and NaCl-treated plants, 5032 genes showed significantly
differences in transcript abundance under salt stress (false discovery rate ≤ 0.001
and |log2Ratio| ≥ 1). These genes were significantly enriched in 29 KEGG pathways and 26 GO
terms. The transcription profiles indicated that genes related to ion transport and
the reactive oxygen species scavenging system were relevant to the morphological and
physiological characteristics of this species. The expression patterns of 30 randomly
selected genes resulted from quantitative real-time PCR were basically consistent
with their transcript abundance changes identified by RNA-seq.

Conclusions

The present study identified potential genes involved in salt tolerance of R. trigyna. The globally sequenced genes covered a considerable proportion of the R. trigyna transcriptome. These data represent a genetic resource for the discovery of genes
related to salt tolerance in this species, and may be a useful source of reference
sequences for closely related taxa. These results can also further our understanding
of salt tolerance in other halophytes surviving under sodic stress.